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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
A panel of ancestry informative markers for the complex five-way admixed South African Coloured population
PLoS ONE, Volume 8, No. 12, Article e82224, Year 2013
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Description
Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's In-statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population. © 2013 Daya et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s001.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s002.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s003.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s004.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s005.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s006.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s007.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s008.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s009.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s010.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s011.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s012.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s013.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s014.xls
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s015.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s016.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s017.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3869660/bin/pone.0082224.s018.zip
Authors & Co-Authors
Daya, Michelle
South Africa, Cape Town
Stellenbosch University, Faculty of Medicine and Health Sciences
van der Merwe, Lize
South Africa, Cape Town
Stellenbosch University, Faculty of Medicine and Health Sciences
South Africa, Tygerberg
South African Medical Research Council
South Africa, Bellville
University of the Western Cape
Galal, Ushma
South Africa, Tygerberg
South African Medical Research Council
Möller, Marlo
South Africa, Cape Town
Stellenbosch University, Faculty of Medicine and Health Sciences
Salie, Muneeb
South Africa, Cape Town
Stellenbosch University, Faculty of Medicine and Health Sciences
Chimusa, Emile R.
South Africa, Cape Town
University of Cape Town
Galanter, Joshua M.
United States, San Francisco
University of California, San Francisco
Van Helden, Paul D.
South Africa, Cape Town
Stellenbosch University, Faculty of Medicine and Health Sciences
Henn, Brenna Mariah
United States, Stony Brook
Stony Brook University
Gignoux, Christopher R.
United States, San Francisco
University of California, San Francisco
Hoal, Eileen G.
South Africa, Cape Town
Stellenbosch University, Faculty of Medicine and Health Sciences
Statistics
Citations: 74
Authors: 11
Affiliations: 6
Identifiers
Doi:
10.1371/journal.pone.0082224
e-ISSN:
19326203
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study
Study Locations
South Africa